bcftools norm don't move some variants to the far left.

[tanger-code]

Hi. I am using bcftools norm command to norm my VCF, but something error happen.

If the vcf file contains the two variants bellow:

Then I use bcftools norm to norm them, and get the following results:

But in fact the del variant can keep moving to the left, like this:

Are there some ways to do this？

[pd3]

Alas, no. The normalization does not take into account modifications introduced by upstream variants. Although this seems desirable at first glance, it becomes less clear when one considers variants in trans.